Starting phenix.real_space_refine (version: dev) on Tue Feb 21 11:49:31 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3j8i_6179/02_2023/3j8i_6179_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3j8i_6179/02_2023/3j8i_6179.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3j8i_6179/02_2023/3j8i_6179.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3j8i_6179/02_2023/3j8i_6179.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3j8i_6179/02_2023/3j8i_6179_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3j8i_6179/02_2023/3j8i_6179_updated.pdb" } resolution = 4.7 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.009 sd= 0.016 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Process input model Symmetric amino acids flipped Residue "D GLU 4": "OE1" <-> "OE2" Residue "D ARG 62": "NH1" <-> "NH2" Residue "D GLU 72": "OE1" <-> "OE2" Residue "D ASP 81": "OD1" <-> "OD2" Residue "D GLU 99": "OE1" <-> "OE2" Residue "D GLU 100": "OE1" <-> "OE2" Residue "D GLU 205": "OE1" <-> "OE2" Residue "D GLU 224": "OE1" <-> "OE2" Residue "D GLU 237": "OE1" <-> "OE2" Residue "D TYR 240": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 253": "OE1" <-> "OE2" Residue "D TYR 279": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 334": "OE1" <-> "OE2" Residue "D ARG 335": "NH1" <-> "NH2" Residue "D TYR 362": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 364": "OE1" <-> "OE2" Residue "D ARG 372": "NH1" <-> "NH2" Residue "D PHE 375": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 4": "OE1" <-> "OE2" Residue "E ARG 62": "NH1" <-> "NH2" Residue "E GLU 72": "OE1" <-> "OE2" Residue "E ASP 81": "OD1" <-> "OD2" Residue "E GLU 99": "OE1" <-> "OE2" Residue "E GLU 100": "OE1" <-> "OE2" Residue "E GLU 205": "OE1" <-> "OE2" Residue "E GLU 224": "OE1" <-> "OE2" Residue "E GLU 237": "OE1" <-> "OE2" Residue "E TYR 240": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 253": "OE1" <-> "OE2" Residue "E GLU 334": "OE1" <-> "OE2" Residue "E ARG 335": "NH1" <-> "NH2" Residue "E TYR 362": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 364": "OE1" <-> "OE2" Residue "E ARG 372": "NH1" <-> "NH2" Residue "E PHE 375": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 4": "OE1" <-> "OE2" Residue "F ARG 62": "NH1" <-> "NH2" Residue "F GLU 72": "OE1" <-> "OE2" Residue "F ASP 81": "OD1" <-> "OD2" Residue "F GLU 99": "OE1" <-> "OE2" Residue "F GLU 100": "OE1" <-> "OE2" Residue "F GLU 205": "OE1" <-> "OE2" Residue "F GLU 224": "OE1" <-> "OE2" Residue "F GLU 237": "OE1" <-> "OE2" Residue "F TYR 240": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 253": "OE1" <-> "OE2" Residue "F TYR 279": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 334": "OE1" <-> "OE2" Residue "F ARG 335": "NH1" <-> "NH2" Residue "F TYR 362": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 364": "OE1" <-> "OE2" Residue "F ARG 372": "NH1" <-> "NH2" Residue "F PHE 375": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 4": "OE1" <-> "OE2" Residue "G ARG 62": "NH1" <-> "NH2" Residue "G GLU 72": "OE1" <-> "OE2" Residue "G ASP 81": "OD1" <-> "OD2" Residue "G GLU 99": "OE1" <-> "OE2" Residue "G GLU 100": "OE1" <-> "OE2" Residue "G GLU 205": "OE1" <-> "OE2" Residue "G GLU 224": "OE1" <-> "OE2" Residue "G GLU 237": "OE1" <-> "OE2" Residue "G TYR 240": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 253": "OE1" <-> "OE2" Residue "G TYR 279": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 334": "OE1" <-> "OE2" Residue "G ARG 335": "NH1" <-> "NH2" Residue "G TYR 362": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 364": "OE1" <-> "OE2" Residue "G ARG 372": "NH1" <-> "NH2" Residue "G PHE 375": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 4": "OE1" <-> "OE2" Residue "H ARG 62": "NH1" <-> "NH2" Residue "H GLU 72": "OE1" <-> "OE2" Residue "H ASP 81": "OD1" <-> "OD2" Residue "H GLU 99": "OE1" <-> "OE2" Residue "H GLU 100": "OE1" <-> "OE2" Residue "H GLU 205": "OE1" <-> "OE2" Residue "H GLU 224": "OE1" <-> "OE2" Residue "H GLU 237": "OE1" <-> "OE2" Residue "H TYR 240": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 253": "OE1" <-> "OE2" Residue "H GLU 334": "OE1" <-> "OE2" Residue "H ARG 335": "NH1" <-> "NH2" Residue "H TYR 362": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 364": "OE1" <-> "OE2" Residue "H ARG 372": "NH1" <-> "NH2" Residue "H PHE 375": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/chem_data/mon_lib" Total number of atoms: 14800 Number of models: 1 Model: "" Number of chains: 10 Chain: "D" Number of atoms: 2932 Number of conformers: 1 Conformer: "" Number of residues, atoms: 375, 2932 Classifications: {'peptide': 375} Link IDs: {'PTRANS': 19, 'TRANS': 355} Chain: "E" Number of atoms: 2932 Number of conformers: 1 Conformer: "" Number of residues, atoms: 375, 2932 Classifications: {'peptide': 375} Link IDs: {'PTRANS': 19, 'TRANS': 355} Chain: "F" Number of atoms: 2932 Number of conformers: 1 Conformer: "" Number of residues, atoms: 375, 2932 Classifications: {'peptide': 375} Link IDs: {'PTRANS': 19, 'TRANS': 355} Chain: "G" Number of atoms: 2932 Number of conformers: 1 Conformer: "" Number of residues, atoms: 375, 2932 Classifications: {'peptide': 375} Link IDs: {'PTRANS': 19, 'TRANS': 355} Chain: "H" Number of atoms: 2932 Number of conformers: 1 Conformer: "" Number of residues, atoms: 375, 2932 Classifications: {'peptide': 375} Link IDs: {'PTRANS': 19, 'TRANS': 355} Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 8.15, per 1000 atoms: 0.55 Number of scatterers: 14800 At special positions: 0 Unit cell: (110.25, 86.1, 194.25, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 105 16.00 P 10 15.00 Mg 5 11.99 O 2870 8.00 N 2490 7.00 C 9320 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 6.23 Conformation dependent library (CDL) restraints added in 2.3 seconds 3730 Ramachandran restraints generated. 1865 Oldfield, 0 Emsley, 1865 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3470 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 76 helices and 15 sheets defined 33.4% alpha, 6.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.32 Creating SS restraints... Processing helix chain 'D' and resid 57 through 60 No H-bonds generated for 'chain 'D' and resid 57 through 60' Processing helix chain 'D' and resid 82 through 90 removed outlier: 3.653A pdb=" N PHE D 90 " --> pdb=" O HIS D 87 " (cutoff:3.500A) Processing helix chain 'D' and resid 113 through 125 Processing helix chain 'D' and resid 137 through 143 removed outlier: 4.118A pdb=" N SER D 141 " --> pdb=" O GLN D 137 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N LEU D 142 " --> pdb=" O ALA D 138 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N TYR D 143 " --> pdb=" O VAL D 139 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 137 through 143' Processing helix chain 'D' and resid 182 through 195 removed outlier: 4.238A pdb=" N THR D 194 " --> pdb=" O MET D 190 " (cutoff:3.500A) removed outlier: 4.651A pdb=" N GLU D 195 " --> pdb=" O LYS D 191 " (cutoff:3.500A) Processing helix chain 'D' and resid 203 through 209 Processing helix chain 'D' and resid 212 through 215 No H-bonds generated for 'chain 'D' and resid 212 through 215' Processing helix chain 'D' and resid 223 through 232 removed outlier: 3.530A pdb=" N MET D 227 " --> pdb=" O GLU D 224 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N ALA D 230 " --> pdb=" O MET D 227 " (cutoff:3.500A) removed outlier: 4.203A pdb=" N ALA D 231 " --> pdb=" O ALA D 228 " (cutoff:3.500A) Processing helix chain 'D' and resid 252 through 262 removed outlier: 3.757A pdb=" N PHE D 255 " --> pdb=" O ASN D 252 " (cutoff:3.500A) removed outlier: 4.643A pdb=" N CYS D 257 " --> pdb=" O ARG D 254 " (cutoff:3.500A) Proline residue: D 258 - end of helix Processing helix chain 'D' and resid 274 through 283 removed outlier: 3.790A pdb=" N TYR D 279 " --> pdb=" O HIS D 275 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N SER D 281 " --> pdb=" O THR D 277 " (cutoff:3.500A) Processing helix chain 'D' and resid 291 through 294 No H-bonds generated for 'chain 'D' and resid 291 through 294' Processing helix chain 'D' and resid 309 through 320 removed outlier: 3.522A pdb=" N THR D 318 " --> pdb=" O GLN D 314 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N LEU D 320 " --> pdb=" O GLU D 316 " (cutoff:3.500A) Processing helix chain 'D' and resid 338 through 347 Processing helix chain 'D' and resid 361 through 364 No H-bonds generated for 'chain 'D' and resid 361 through 364' Processing helix chain 'D' and resid 367 through 371 removed outlier: 3.551A pdb=" N HIS D 371 " --> pdb=" O PRO D 367 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 367 through 371' Processing helix chain 'E' and resid 57 through 60 No H-bonds generated for 'chain 'E' and resid 57 through 60' Processing helix chain 'E' and resid 82 through 90 removed outlier: 3.570A pdb=" N PHE E 90 " --> pdb=" O HIS E 87 " (cutoff:3.500A) Processing helix chain 'E' and resid 113 through 125 Processing helix chain 'E' and resid 137 through 143 removed outlier: 4.065A pdb=" N SER E 141 " --> pdb=" O GLN E 137 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N LEU E 142 " --> pdb=" O ALA E 138 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N TYR E 143 " --> pdb=" O VAL E 139 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 137 through 143' Processing helix chain 'E' and resid 182 through 195 removed outlier: 4.228A pdb=" N THR E 194 " --> pdb=" O MET E 190 " (cutoff:3.500A) removed outlier: 4.643A pdb=" N GLU E 195 " --> pdb=" O LYS E 191 " (cutoff:3.500A) Processing helix chain 'E' and resid 203 through 209 Processing helix chain 'E' and resid 212 through 215 No H-bonds generated for 'chain 'E' and resid 212 through 215' Processing helix chain 'E' and resid 223 through 232 removed outlier: 3.541A pdb=" N MET E 227 " --> pdb=" O GLU E 224 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N THR E 229 " --> pdb=" O GLU E 226 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N ALA E 230 " --> pdb=" O MET E 227 " (cutoff:3.500A) removed outlier: 4.156A pdb=" N ALA E 231 " --> pdb=" O ALA E 228 " (cutoff:3.500A) Processing helix chain 'E' and resid 252 through 262 removed outlier: 3.717A pdb=" N PHE E 255 " --> pdb=" O ASN E 252 " (cutoff:3.500A) removed outlier: 4.635A pdb=" N CYS E 257 " --> pdb=" O ARG E 254 " (cutoff:3.500A) Proline residue: E 258 - end of helix Processing helix chain 'E' and resid 274 through 283 removed outlier: 3.811A pdb=" N TYR E 279 " --> pdb=" O HIS E 275 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N SER E 281 " --> pdb=" O THR E 277 " (cutoff:3.500A) Processing helix chain 'E' and resid 291 through 294 No H-bonds generated for 'chain 'E' and resid 291 through 294' Processing helix chain 'E' and resid 309 through 320 removed outlier: 3.537A pdb=" N THR E 318 " --> pdb=" O GLN E 314 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N LEU E 320 " --> pdb=" O GLU E 316 " (cutoff:3.500A) Processing helix chain 'E' and resid 338 through 347 Processing helix chain 'E' and resid 361 through 364 No H-bonds generated for 'chain 'E' and resid 361 through 364' Processing helix chain 'E' and resid 367 through 371 removed outlier: 3.513A pdb=" N HIS E 371 " --> pdb=" O PRO E 367 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 367 through 371' Processing helix chain 'F' and resid 57 through 60 No H-bonds generated for 'chain 'F' and resid 57 through 60' Processing helix chain 'F' and resid 82 through 90 removed outlier: 3.614A pdb=" N PHE F 90 " --> pdb=" O HIS F 87 " (cutoff:3.500A) Processing helix chain 'F' and resid 113 through 125 Processing helix chain 'F' and resid 137 through 143 removed outlier: 4.079A pdb=" N SER F 141 " --> pdb=" O GLN F 137 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N LEU F 142 " --> pdb=" O ALA F 138 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N TYR F 143 " --> pdb=" O VAL F 139 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 137 through 143' Processing helix chain 'F' and resid 182 through 195 removed outlier: 4.305A pdb=" N THR F 194 " --> pdb=" O MET F 190 " (cutoff:3.500A) removed outlier: 4.666A pdb=" N GLU F 195 " --> pdb=" O LYS F 191 " (cutoff:3.500A) Processing helix chain 'F' and resid 203 through 209 Processing helix chain 'F' and resid 212 through 215 No H-bonds generated for 'chain 'F' and resid 212 through 215' Processing helix chain 'F' and resid 223 through 232 removed outlier: 3.558A pdb=" N MET F 227 " --> pdb=" O GLU F 224 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N ALA F 230 " --> pdb=" O MET F 227 " (cutoff:3.500A) removed outlier: 4.223A pdb=" N ALA F 231 " --> pdb=" O ALA F 228 " (cutoff:3.500A) Processing helix chain 'F' and resid 252 through 262 removed outlier: 3.733A pdb=" N PHE F 255 " --> pdb=" O ASN F 252 " (cutoff:3.500A) removed outlier: 4.573A pdb=" N CYS F 257 " --> pdb=" O ARG F 254 " (cutoff:3.500A) Proline residue: F 258 - end of helix Processing helix chain 'F' and resid 274 through 283 removed outlier: 3.851A pdb=" N TYR F 279 " --> pdb=" O HIS F 275 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N SER F 281 " --> pdb=" O THR F 277 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ILE F 282 " --> pdb=" O THR F 278 " (cutoff:3.500A) Processing helix chain 'F' and resid 291 through 296 Processing helix chain 'F' and resid 309 through 320 removed outlier: 3.609A pdb=" N THR F 318 " --> pdb=" O GLN F 314 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N LEU F 320 " --> pdb=" O GLU F 316 " (cutoff:3.500A) Processing helix chain 'F' and resid 338 through 347 Processing helix chain 'F' and resid 361 through 364 No H-bonds generated for 'chain 'F' and resid 361 through 364' Processing helix chain 'F' and resid 367 through 371 removed outlier: 3.534A pdb=" N HIS F 371 " --> pdb=" O PRO F 367 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 367 through 371' Processing helix chain 'G' and resid 57 through 60 No H-bonds generated for 'chain 'G' and resid 57 through 60' Processing helix chain 'G' and resid 82 through 90 removed outlier: 3.612A pdb=" N PHE G 90 " --> pdb=" O HIS G 87 " (cutoff:3.500A) Processing helix chain 'G' and resid 113 through 125 Processing helix chain 'G' and resid 137 through 143 removed outlier: 4.050A pdb=" N SER G 141 " --> pdb=" O GLN G 137 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N LEU G 142 " --> pdb=" O ALA G 138 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N TYR G 143 " --> pdb=" O VAL G 139 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 137 through 143' Processing helix chain 'G' and resid 172 through 174 No H-bonds generated for 'chain 'G' and resid 172 through 174' Processing helix chain 'G' and resid 182 through 195 removed outlier: 4.226A pdb=" N THR G 194 " --> pdb=" O MET G 190 " (cutoff:3.500A) removed outlier: 4.644A pdb=" N GLU G 195 " --> pdb=" O LYS G 191 " (cutoff:3.500A) Processing helix chain 'G' and resid 203 through 209 Processing helix chain 'G' and resid 212 through 215 No H-bonds generated for 'chain 'G' and resid 212 through 215' Processing helix chain 'G' and resid 223 through 232 removed outlier: 3.553A pdb=" N MET G 227 " --> pdb=" O GLU G 224 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N ALA G 230 " --> pdb=" O MET G 227 " (cutoff:3.500A) removed outlier: 4.223A pdb=" N ALA G 231 " --> pdb=" O ALA G 228 " (cutoff:3.500A) Processing helix chain 'G' and resid 252 through 262 removed outlier: 3.747A pdb=" N PHE G 255 " --> pdb=" O ASN G 252 " (cutoff:3.500A) removed outlier: 4.656A pdb=" N CYS G 257 " --> pdb=" O ARG G 254 " (cutoff:3.500A) Proline residue: G 258 - end of helix Processing helix chain 'G' and resid 274 through 283 removed outlier: 3.767A pdb=" N TYR G 279 " --> pdb=" O HIS G 275 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N SER G 281 " --> pdb=" O THR G 277 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ILE G 282 " --> pdb=" O THR G 278 " (cutoff:3.500A) Processing helix chain 'G' and resid 291 through 295 Processing helix chain 'G' and resid 309 through 320 removed outlier: 3.570A pdb=" N THR G 318 " --> pdb=" O GLN G 314 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N LEU G 320 " --> pdb=" O GLU G 316 " (cutoff:3.500A) Processing helix chain 'G' and resid 338 through 347 Processing helix chain 'G' and resid 361 through 364 No H-bonds generated for 'chain 'G' and resid 361 through 364' Processing helix chain 'G' and resid 367 through 371 removed outlier: 3.560A pdb=" N HIS G 371 " --> pdb=" O PRO G 367 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 367 through 371' Processing helix chain 'H' and resid 57 through 60 No H-bonds generated for 'chain 'H' and resid 57 through 60' Processing helix chain 'H' and resid 82 through 90 removed outlier: 3.590A pdb=" N PHE H 90 " --> pdb=" O HIS H 87 " (cutoff:3.500A) Processing helix chain 'H' and resid 113 through 126 Processing helix chain 'H' and resid 137 through 143 removed outlier: 4.079A pdb=" N SER H 141 " --> pdb=" O GLN H 137 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N LEU H 142 " --> pdb=" O ALA H 138 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N TYR H 143 " --> pdb=" O VAL H 139 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 137 through 143' Processing helix chain 'H' and resid 182 through 195 removed outlier: 4.229A pdb=" N THR H 194 " --> pdb=" O MET H 190 " (cutoff:3.500A) removed outlier: 4.630A pdb=" N GLU H 195 " --> pdb=" O LYS H 191 " (cutoff:3.500A) Processing helix chain 'H' and resid 203 through 209 Processing helix chain 'H' and resid 212 through 215 No H-bonds generated for 'chain 'H' and resid 212 through 215' Processing helix chain 'H' and resid 223 through 232 removed outlier: 3.523A pdb=" N MET H 227 " --> pdb=" O GLU H 224 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N ALA H 230 " --> pdb=" O MET H 227 " (cutoff:3.500A) removed outlier: 4.175A pdb=" N ALA H 231 " --> pdb=" O ALA H 228 " (cutoff:3.500A) Processing helix chain 'H' and resid 252 through 262 removed outlier: 3.736A pdb=" N PHE H 255 " --> pdb=" O ASN H 252 " (cutoff:3.500A) removed outlier: 4.608A pdb=" N CYS H 257 " --> pdb=" O ARG H 254 " (cutoff:3.500A) Proline residue: H 258 - end of helix Processing helix chain 'H' and resid 274 through 283 removed outlier: 3.871A pdb=" N TYR H 279 " --> pdb=" O HIS H 275 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N SER H 281 " --> pdb=" O THR H 277 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ILE H 282 " --> pdb=" O THR H 278 " (cutoff:3.500A) Processing helix chain 'H' and resid 291 through 294 No H-bonds generated for 'chain 'H' and resid 291 through 294' Processing helix chain 'H' and resid 309 through 320 removed outlier: 3.560A pdb=" N THR H 318 " --> pdb=" O GLN H 314 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N LEU H 320 " --> pdb=" O GLU H 316 " (cutoff:3.500A) Processing helix chain 'H' and resid 338 through 347 Processing helix chain 'H' and resid 361 through 364 No H-bonds generated for 'chain 'H' and resid 361 through 364' Processing helix chain 'H' and resid 367 through 371 removed outlier: 3.554A pdb=" N HIS H 371 " --> pdb=" O PRO H 367 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 367 through 371' Processing sheet with id= A, first strand: chain 'D' and resid 7 through 9 removed outlier: 3.861A pdb=" N TYR D 133 " --> pdb=" O THR D 103 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'D' and resid 16 through 19 Processing sheet with id= C, first strand: chain 'D' and resid 162 through 165 removed outlier: 3.631A pdb=" N VAL D 163 " --> pdb=" O VAL D 152 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N VAL D 152 " --> pdb=" O VAL D 163 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'E' and resid 7 through 9 removed outlier: 3.811A pdb=" N TYR E 133 " --> pdb=" O THR E 103 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'E' and resid 16 through 19 Processing sheet with id= F, first strand: chain 'E' and resid 162 through 165 removed outlier: 3.629A pdb=" N VAL E 163 " --> pdb=" O VAL E 152 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N VAL E 152 " --> pdb=" O VAL E 163 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'F' and resid 7 through 9 removed outlier: 3.855A pdb=" N TYR F 133 " --> pdb=" O THR F 103 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'F' and resid 16 through 19 Processing sheet with id= I, first strand: chain 'F' and resid 162 through 165 removed outlier: 3.608A pdb=" N VAL F 163 " --> pdb=" O VAL F 152 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N VAL F 152 " --> pdb=" O VAL F 163 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'G' and resid 7 through 9 removed outlier: 3.858A pdb=" N TYR G 133 " --> pdb=" O THR G 103 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'G' and resid 16 through 19 Processing sheet with id= L, first strand: chain 'G' and resid 162 through 165 removed outlier: 3.649A pdb=" N VAL G 163 " --> pdb=" O VAL G 152 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N VAL G 152 " --> pdb=" O VAL G 163 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'H' and resid 7 through 9 removed outlier: 3.838A pdb=" N TYR H 133 " --> pdb=" O THR H 103 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'H' and resid 16 through 19 Processing sheet with id= O, first strand: chain 'H' and resid 162 through 165 removed outlier: 3.643A pdb=" N VAL H 163 " --> pdb=" O VAL H 152 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N VAL H 152 " --> pdb=" O VAL H 163 " (cutoff:3.500A) 295 hydrogen bonds defined for protein. 678 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.59 Time building geometry restraints manager: 6.66 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.34: 4526 1.34 - 1.48: 4024 1.48 - 1.63: 6385 1.63 - 1.77: 21 1.77 - 1.91: 164 Bond restraints: 15120 Sorted by residual: bond pdb=" C LEU D 171 " pdb=" N PRO D 172 " ideal model delta sigma weight residual 1.331 1.383 -0.052 7.90e-03 1.60e+04 4.29e+01 bond pdb=" C LEU H 171 " pdb=" N PRO H 172 " ideal model delta sigma weight residual 1.331 1.382 -0.050 7.90e-03 1.60e+04 4.05e+01 bond pdb=" C LEU F 171 " pdb=" N PRO F 172 " ideal model delta sigma weight residual 1.331 1.379 -0.047 7.90e-03 1.60e+04 3.55e+01 bond pdb=" CA ILE E 250 " pdb=" C ILE E 250 " ideal model delta sigma weight residual 1.526 1.474 0.052 9.00e-03 1.23e+04 3.32e+01 bond pdb=" C LEU E 171 " pdb=" N PRO E 172 " ideal model delta sigma weight residual 1.331 1.376 -0.045 7.90e-03 1.60e+04 3.24e+01 ... (remaining 15115 not shown) Histogram of bond angle deviations from ideal: 98.44 - 105.87: 547 105.87 - 113.29: 7617 113.29 - 120.72: 6773 120.72 - 128.15: 5453 128.15 - 135.58: 125 Bond angle restraints: 20515 Sorted by residual: angle pdb=" C VAL F 129 " pdb=" N PRO F 130 " pdb=" CA PRO F 130 " ideal model delta sigma weight residual 119.19 126.79 -7.60 1.06e+00 8.90e-01 5.13e+01 angle pdb=" C ALA D 108 " pdb=" N PRO D 109 " pdb=" CA PRO D 109 " ideal model delta sigma weight residual 119.78 127.02 -7.24 1.03e+00 9.43e-01 4.94e+01 angle pdb=" N ALA G 138 " pdb=" CA ALA G 138 " pdb=" C ALA G 138 " ideal model delta sigma weight residual 111.28 118.53 -7.25 1.09e+00 8.42e-01 4.42e+01 angle pdb=" C ALA G 108 " pdb=" N PRO G 109 " pdb=" CA PRO G 109 " ideal model delta sigma weight residual 119.78 126.55 -6.77 1.03e+00 9.43e-01 4.32e+01 angle pdb=" N ALA D 138 " pdb=" CA ALA D 138 " pdb=" C ALA D 138 " ideal model delta sigma weight residual 111.36 118.09 -6.73 1.09e+00 8.42e-01 3.81e+01 ... (remaining 20510 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.49: 8650 35.49 - 70.97: 411 70.97 - 106.46: 34 106.46 - 141.94: 5 141.94 - 177.43: 5 Dihedral angle restraints: 9105 sinusoidal: 3685 harmonic: 5420 Sorted by residual: dihedral pdb=" C5' ADP G 401 " pdb=" O5' ADP G 401 " pdb=" PA ADP G 401 " pdb=" O2A ADP G 401 " ideal model delta sinusoidal sigma weight residual -60.00 117.43 -177.43 1 2.00e+01 2.50e-03 4.80e+01 dihedral pdb=" C5' ADP D 401 " pdb=" O5' ADP D 401 " pdb=" PA ADP D 401 " pdb=" O2A ADP D 401 " ideal model delta sinusoidal sigma weight residual -60.00 117.43 -177.43 1 2.00e+01 2.50e-03 4.80e+01 dihedral pdb=" C5' ADP F 401 " pdb=" O5' ADP F 401 " pdb=" PA ADP F 401 " pdb=" O2A ADP F 401 " ideal model delta sinusoidal sigma weight residual -60.00 117.33 -177.32 1 2.00e+01 2.50e-03 4.80e+01 ... (remaining 9102 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.093: 1407 0.093 - 0.185: 657 0.185 - 0.278: 181 0.278 - 0.370: 24 0.370 - 0.463: 6 Chirality restraints: 2275 Sorted by residual: chirality pdb=" CA PRO E 243 " pdb=" N PRO E 243 " pdb=" C PRO E 243 " pdb=" CB PRO E 243 " both_signs ideal model delta sigma weight residual False 2.72 2.26 0.46 2.00e-01 2.50e+01 5.36e+00 chirality pdb=" CA PRO F 243 " pdb=" N PRO F 243 " pdb=" C PRO F 243 " pdb=" CB PRO F 243 " both_signs ideal model delta sigma weight residual False 2.72 2.27 0.45 2.00e-01 2.50e+01 5.03e+00 chirality pdb=" CA PRO H 243 " pdb=" N PRO H 243 " pdb=" C PRO H 243 " pdb=" CB PRO H 243 " both_signs ideal model delta sigma weight residual False 2.72 2.29 0.43 2.00e-01 2.50e+01 4.54e+00 ... (remaining 2272 not shown) Planarity restraints: 2630 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR D 166 " -0.071 2.00e-02 2.50e+03 3.56e-02 2.53e+01 pdb=" CG TYR D 166 " 0.035 2.00e-02 2.50e+03 pdb=" CD1 TYR D 166 " 0.031 2.00e-02 2.50e+03 pdb=" CD2 TYR D 166 " 0.033 2.00e-02 2.50e+03 pdb=" CE1 TYR D 166 " 0.009 2.00e-02 2.50e+03 pdb=" CE2 TYR D 166 " 0.008 2.00e-02 2.50e+03 pdb=" CZ TYR D 166 " -0.005 2.00e-02 2.50e+03 pdb=" OH TYR D 166 " -0.041 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR E 166 " 0.061 2.00e-02 2.50e+03 3.07e-02 1.88e+01 pdb=" CG TYR E 166 " -0.031 2.00e-02 2.50e+03 pdb=" CD1 TYR E 166 " -0.027 2.00e-02 2.50e+03 pdb=" CD2 TYR E 166 " -0.028 2.00e-02 2.50e+03 pdb=" CE1 TYR E 166 " -0.008 2.00e-02 2.50e+03 pdb=" CE2 TYR E 166 " -0.007 2.00e-02 2.50e+03 pdb=" CZ TYR E 166 " 0.005 2.00e-02 2.50e+03 pdb=" OH TYR E 166 " 0.035 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR H 166 " -0.060 2.00e-02 2.50e+03 3.03e-02 1.83e+01 pdb=" CG TYR H 166 " 0.034 2.00e-02 2.50e+03 pdb=" CD1 TYR H 166 " 0.028 2.00e-02 2.50e+03 pdb=" CD2 TYR H 166 " 0.029 2.00e-02 2.50e+03 pdb=" CE1 TYR H 166 " 0.004 2.00e-02 2.50e+03 pdb=" CE2 TYR H 166 " 0.003 2.00e-02 2.50e+03 pdb=" CZ TYR H 166 " -0.011 2.00e-02 2.50e+03 pdb=" OH TYR H 166 " -0.027 2.00e-02 2.50e+03 ... (remaining 2627 not shown) Histogram of nonbonded interaction distances: 2.13 - 2.68: 801 2.68 - 3.24: 17004 3.24 - 3.79: 24798 3.79 - 4.35: 32535 4.35 - 4.90: 50182 Nonbonded interactions: 125320 Sorted by model distance: nonbonded pdb=" O SER F 350 " pdb=" N PHE F 352 " model vdw 2.125 2.520 nonbonded pdb=" O TYR H 362 " pdb=" O ALA H 365 " model vdw 2.131 3.040 nonbonded pdb=" O TYR F 362 " pdb=" O ALA F 365 " model vdw 2.140 3.040 nonbonded pdb=" O TYR G 362 " pdb=" O ALA G 365 " model vdw 2.154 3.040 nonbonded pdb=" O SER D 350 " pdb=" N PHE D 352 " model vdw 2.160 2.520 ... (remaining 125315 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' } Set up NCS constraints Number of NCS constrained groups: 1 pdb_interpretation.ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' } Set refine NCS operators NCS operators will be refined. Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 10 5.49 5 Mg 5 5.21 5 S 105 5.16 5 C 9320 2.51 5 N 2490 2.21 5 O 2870 1.98 5 sf(0) = scattering factor at diffraction angle 0. Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.220 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 2.560 Check model and map are aligned: 0.230 Process input model: 38.570 Find NCS groups from input model: 0.920 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Set scattering table: 0.130 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.810 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 45.530 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7622 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.018 0.120 15120 Z= 1.168 Angle : 1.668 11.796 20515 Z= 1.105 Chirality : 0.109 0.463 2275 Planarity : 0.007 0.098 2630 Dihedral : 19.470 177.430 5635 Min Nonbonded Distance : 2.125 Molprobity Statistics. All-atom Clashscore : 76.17 Ramachandran Plot: Outliers : 6.06 % Allowed : 6.43 % Favored : 87.51 % Rotamer Outliers : 14.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.59 (0.17), residues: 1865 helix: -0.26 (0.22), residues: 500 sheet: 0.08 (0.37), residues: 205 loop : -1.71 (0.16), residues: 1160 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3730 Ramachandran restraints generated. 1865 Oldfield, 0 Emsley, 1865 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3730 Ramachandran restraints generated. 1865 Oldfield, 0 Emsley, 1865 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 318 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 60 time to evaluate : 0.362 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 46 outliers final: 19 residues processed: 96 average time/residue: 0.1680 time to fit residues: 19.2254 Evaluate side-chains 57 residues out of total 318 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 38 time to evaluate : 0.379 Switching outliers to nearest non-outliers outliers start: 19 outliers final: 0 residues processed: 19 average time/residue: 0.0667 time to fit residues: 2.1988 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 156 optimal weight: 10.0000 chunk 140 optimal weight: 20.0000 chunk 77 optimal weight: 4.9990 chunk 47 optimal weight: 0.5980 chunk 94 optimal weight: 20.0000 chunk 74 optimal weight: 40.0000 chunk 145 optimal weight: 20.0000 chunk 56 optimal weight: 5.9990 chunk 88 optimal weight: 2.9990 chunk 107 optimal weight: 9.9990 chunk 168 optimal weight: 20.0000 overall best weight: 4.9188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 59 GLN ** F 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 137 GLN F 162 ASN F 296 ASN ** F 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7484 moved from start: 0.4260 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.034 15120 Z= 0.259 Angle : 0.894 9.045 20515 Z= 0.450 Chirality : 0.047 0.197 2275 Planarity : 0.007 0.072 2630 Dihedral : 8.742 117.313 2095 Min Nonbonded Distance : 2.195 Molprobity Statistics. All-atom Clashscore : 28.67 Ramachandran Plot: Outliers : 2.14 % Allowed : 10.46 % Favored : 87.40 % Rotamer Outliers : 1.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.68 (0.19), residues: 1865 helix: -0.34 (0.21), residues: 595 sheet: 0.13 (0.37), residues: 220 loop : -1.92 (0.18), residues: 1050 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2984 Ramachandran restraints generated. 1492 Oldfield, 0 Emsley, 1492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2984 Ramachandran restraints generated. 1492 Oldfield, 0 Emsley, 1492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 318 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 68 time to evaluate : 0.366 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 4 outliers final: 1 residues processed: 70 average time/residue: 0.1628 time to fit residues: 13.6990 Evaluate side-chains 44 residues out of total 318 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 43 time to evaluate : 0.373 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0335 time to fit residues: 0.5752 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 93 optimal weight: 3.9990 chunk 52 optimal weight: 0.9990 chunk 139 optimal weight: 0.6980 chunk 114 optimal weight: 20.0000 chunk 46 optimal weight: 0.0970 chunk 168 optimal weight: 20.0000 chunk 181 optimal weight: 10.0000 chunk 149 optimal weight: 0.0870 chunk 166 optimal weight: 8.9990 chunk 57 optimal weight: 20.0000 chunk 135 optimal weight: 7.9990 overall best weight: 1.1760 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 314 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7455 moved from start: 0.5282 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.035 15120 Z= 0.198 Angle : 0.809 7.631 20515 Z= 0.401 Chirality : 0.046 0.174 2275 Planarity : 0.005 0.043 2630 Dihedral : 7.955 102.514 2095 Min Nonbonded Distance : 2.209 Molprobity Statistics. All-atom Clashscore : 23.42 Ramachandran Plot: Outliers : 1.34 % Allowed : 10.19 % Favored : 88.47 % Rotamer Outliers : 0.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.94 (0.18), residues: 1865 helix: -1.18 (0.20), residues: 600 sheet: -0.13 (0.44), residues: 155 loop : -1.55 (0.18), residues: 1110 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2984 Ramachandran restraints generated. 1492 Oldfield, 0 Emsley, 1492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2984 Ramachandran restraints generated. 1492 Oldfield, 0 Emsley, 1492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 318 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 62 time to evaluate : 0.384 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 0 residues processed: 63 average time/residue: 0.1192 time to fit residues: 9.7069 Evaluate side-chains 41 residues out of total 318 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 41 time to evaluate : 0.318 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.4332 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 166 optimal weight: 9.9990 chunk 126 optimal weight: 0.8980 chunk 87 optimal weight: 1.9990 chunk 18 optimal weight: 9.9990 chunk 80 optimal weight: 20.0000 chunk 113 optimal weight: 5.9990 chunk 168 optimal weight: 20.0000 chunk 178 optimal weight: 5.9990 chunk 88 optimal weight: 0.0270 chunk 160 optimal weight: 0.0070 chunk 48 optimal weight: 20.0000 overall best weight: 1.7860 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 297 ASN ** F 371 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7476 moved from start: 0.5865 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.037 15120 Z= 0.182 Angle : 0.791 9.391 20515 Z= 0.390 Chirality : 0.043 0.148 2275 Planarity : 0.005 0.039 2630 Dihedral : 6.767 71.008 2095 Min Nonbonded Distance : 1.942 Molprobity Statistics. All-atom Clashscore : 21.79 Ramachandran Plot: Outliers : 1.07 % Allowed : 11.26 % Favored : 87.67 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.82 (0.18), residues: 1865 helix: -0.76 (0.21), residues: 555 sheet: -0.81 (0.36), residues: 215 loop : -1.56 (0.18), residues: 1095 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2984 Ramachandran restraints generated. 1492 Oldfield, 0 Emsley, 1492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2984 Ramachandran restraints generated. 1492 Oldfield, 0 Emsley, 1492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 52 residues out of total 318 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 52 time to evaluate : 0.366 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 52 average time/residue: 0.1316 time to fit residues: 8.7432 Evaluate side-chains 42 residues out of total 318 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 42 time to evaluate : 0.363 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.4866 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 148 optimal weight: 30.0000 chunk 101 optimal weight: 10.0000 chunk 2 optimal weight: 8.9990 chunk 133 optimal weight: 30.0000 chunk 73 optimal weight: 1.9990 chunk 152 optimal weight: 0.4980 chunk 123 optimal weight: 0.0010 chunk 0 optimal weight: 30.0000 chunk 91 optimal weight: 2.9990 chunk 160 optimal weight: 0.0980 chunk 45 optimal weight: 3.9990 overall best weight: 1.1190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 115 ASN F 173 HIS ** F 371 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7440 moved from start: 0.6376 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.029 15120 Z= 0.160 Angle : 0.755 7.518 20515 Z= 0.367 Chirality : 0.043 0.161 2275 Planarity : 0.005 0.037 2630 Dihedral : 6.096 52.672 2095 Min Nonbonded Distance : 2.004 Molprobity Statistics. All-atom Clashscore : 19.16 Ramachandran Plot: Outliers : 1.07 % Allowed : 8.85 % Favored : 90.08 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.72 (0.19), residues: 1865 helix: -0.63 (0.22), residues: 555 sheet: -0.67 (0.35), residues: 225 loop : -1.54 (0.18), residues: 1085 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2984 Ramachandran restraints generated. 1492 Oldfield, 0 Emsley, 1492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2984 Ramachandran restraints generated. 1492 Oldfield, 0 Emsley, 1492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 318 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 55 time to evaluate : 0.333 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 55 average time/residue: 0.1361 time to fit residues: 9.4202 Evaluate side-chains 43 residues out of total 318 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 43 time to evaluate : 0.329 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.4655 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 60 optimal weight: 6.9990 chunk 161 optimal weight: 1.9990 chunk 35 optimal weight: 20.0000 chunk 104 optimal weight: 0.0010 chunk 44 optimal weight: 20.0000 chunk 178 optimal weight: 4.9990 chunk 148 optimal weight: 30.0000 chunk 82 optimal weight: 8.9990 chunk 14 optimal weight: 20.0000 chunk 59 optimal weight: 30.0000 chunk 93 optimal weight: 10.0000 overall best weight: 4.5994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 371 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7540 moved from start: 0.6601 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.034 15120 Z= 0.194 Angle : 0.765 10.741 20515 Z= 0.379 Chirality : 0.043 0.138 2275 Planarity : 0.005 0.038 2630 Dihedral : 6.020 39.940 2095 Min Nonbonded Distance : 1.979 Molprobity Statistics. All-atom Clashscore : 21.04 Ramachandran Plot: Outliers : 1.07 % Allowed : 9.92 % Favored : 89.01 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.78 (0.19), residues: 1865 helix: -0.78 (0.21), residues: 560 sheet: -0.65 (0.35), residues: 210 loop : -1.53 (0.18), residues: 1095 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2984 Ramachandran restraints generated. 1492 Oldfield, 0 Emsley, 1492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2984 Ramachandran restraints generated. 1492 Oldfield, 0 Emsley, 1492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 48 residues out of total 318 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 48 time to evaluate : 0.286 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 48 average time/residue: 0.1271 time to fit residues: 7.7808 Evaluate side-chains 39 residues out of total 318 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 39 time to evaluate : 0.327 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.4483 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 172 optimal weight: 8.9990 chunk 20 optimal weight: 20.0000 chunk 101 optimal weight: 6.9990 chunk 130 optimal weight: 5.9990 chunk 150 optimal weight: 7.9990 chunk 99 optimal weight: 4.9990 chunk 178 optimal weight: 0.8980 chunk 111 optimal weight: 30.0000 chunk 108 optimal weight: 20.0000 chunk 82 optimal weight: 0.9990 chunk 110 optimal weight: 0.6980 overall best weight: 2.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 371 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7521 moved from start: 0.6852 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.029 15120 Z= 0.161 Angle : 0.739 8.669 20515 Z= 0.362 Chirality : 0.044 0.271 2275 Planarity : 0.004 0.038 2630 Dihedral : 5.793 34.245 2095 Min Nonbonded Distance : 2.043 Molprobity Statistics. All-atom Clashscore : 19.23 Ramachandran Plot: Outliers : 1.07 % Allowed : 9.92 % Favored : 89.01 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.77 (0.19), residues: 1865 helix: -0.78 (0.21), residues: 560 sheet: -0.50 (0.34), residues: 230 loop : -1.57 (0.18), residues: 1075 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2984 Ramachandran restraints generated. 1492 Oldfield, 0 Emsley, 1492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2984 Ramachandran restraints generated. 1492 Oldfield, 0 Emsley, 1492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 48 residues out of total 318 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 48 time to evaluate : 0.363 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 48 average time/residue: 0.1138 time to fit residues: 7.1261 Evaluate side-chains 37 residues out of total 318 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 37 time to evaluate : 0.277 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.4909 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 71 optimal weight: 20.0000 chunk 106 optimal weight: 1.9990 chunk 53 optimal weight: 0.0980 chunk 35 optimal weight: 1.9990 chunk 34 optimal weight: 30.0000 chunk 113 optimal weight: 0.0370 chunk 121 optimal weight: 2.9990 chunk 88 optimal weight: 0.5980 chunk 16 optimal weight: 4.9990 chunk 140 optimal weight: 20.0000 chunk 162 optimal weight: 3.9990 overall best weight: 0.9462 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 101 HIS ** F 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 173 HIS ** F 371 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7467 moved from start: 0.7255 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.029 15120 Z= 0.164 Angle : 0.766 9.996 20515 Z= 0.371 Chirality : 0.044 0.248 2275 Planarity : 0.004 0.039 2630 Dihedral : 5.838 32.811 2095 Min Nonbonded Distance : 2.060 Molprobity Statistics. All-atom Clashscore : 18.48 Ramachandran Plot: Outliers : 0.80 % Allowed : 11.26 % Favored : 87.94 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.77 (0.19), residues: 1865 helix: -0.73 (0.21), residues: 560 sheet: -0.07 (0.45), residues: 140 loop : -1.60 (0.17), residues: 1165 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2984 Ramachandran restraints generated. 1492 Oldfield, 0 Emsley, 1492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2984 Ramachandran restraints generated. 1492 Oldfield, 0 Emsley, 1492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 50 residues out of total 318 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 50 time to evaluate : 0.376 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 50 average time/residue: 0.1185 time to fit residues: 7.7758 Evaluate side-chains 38 residues out of total 318 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 38 time to evaluate : 0.387 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.4512 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 170 optimal weight: 4.9990 chunk 155 optimal weight: 20.0000 chunk 166 optimal weight: 8.9990 chunk 100 optimal weight: 20.0000 chunk 72 optimal weight: 0.6980 chunk 130 optimal weight: 0.9990 chunk 50 optimal weight: 5.9990 chunk 150 optimal weight: 0.0070 chunk 157 optimal weight: 6.9990 chunk 165 optimal weight: 2.9990 chunk 109 optimal weight: 0.4980 overall best weight: 1.0402 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 371 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7437 moved from start: 0.7559 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.031 15120 Z= 0.159 Angle : 0.761 9.470 20515 Z= 0.365 Chirality : 0.044 0.230 2275 Planarity : 0.004 0.039 2630 Dihedral : 5.601 31.971 2095 Min Nonbonded Distance : 2.063 Molprobity Statistics. All-atom Clashscore : 17.73 Ramachandran Plot: Outliers : 0.80 % Allowed : 10.19 % Favored : 89.01 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.75 (0.18), residues: 1865 helix: -0.70 (0.21), residues: 560 sheet: -0.30 (0.35), residues: 205 loop : -1.62 (0.18), residues: 1100 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2984 Ramachandran restraints generated. 1492 Oldfield, 0 Emsley, 1492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2984 Ramachandran restraints generated. 1492 Oldfield, 0 Emsley, 1492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 49 residues out of total 318 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 49 time to evaluate : 0.363 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 49 average time/residue: 0.1386 time to fit residues: 8.6187 Evaluate side-chains 34 residues out of total 318 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 34 time to evaluate : 0.384 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.4652 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 175 optimal weight: 20.0000 chunk 107 optimal weight: 0.6980 chunk 83 optimal weight: 3.9990 chunk 122 optimal weight: 8.9990 chunk 184 optimal weight: 1.9990 chunk 169 optimal weight: 0.6980 chunk 146 optimal weight: 8.9990 chunk 15 optimal weight: 0.0970 chunk 113 optimal weight: 0.0870 chunk 89 optimal weight: 0.0970 chunk 116 optimal weight: 20.0000 overall best weight: 0.3354 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 297 ASN ** F 371 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7379 moved from start: 0.7983 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.023 15120 Z= 0.174 Angle : 0.814 12.495 20515 Z= 0.392 Chirality : 0.044 0.236 2275 Planarity : 0.005 0.039 2630 Dihedral : 5.641 32.550 2095 Min Nonbonded Distance : 2.089 Molprobity Statistics. All-atom Clashscore : 17.15 Ramachandran Plot: Outliers : 0.54 % Allowed : 12.06 % Favored : 87.40 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.94 (0.19), residues: 1865 helix: -0.78 (0.21), residues: 560 sheet: -0.19 (0.32), residues: 255 loop : -1.91 (0.18), residues: 1050 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2984 Ramachandran restraints generated. 1492 Oldfield, 0 Emsley, 1492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2984 Ramachandran restraints generated. 1492 Oldfield, 0 Emsley, 1492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 49 residues out of total 318 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 49 time to evaluate : 0.383 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 49 average time/residue: 0.1708 time to fit residues: 10.2054 Evaluate side-chains 33 residues out of total 318 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 33 time to evaluate : 0.489 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.5058 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 156 optimal weight: 1.9990 chunk 44 optimal weight: 0.9980 chunk 135 optimal weight: 0.6980 chunk 21 optimal weight: 20.0000 chunk 40 optimal weight: 0.1980 chunk 146 optimal weight: 3.9990 chunk 61 optimal weight: 5.9990 chunk 150 optimal weight: 0.0000 chunk 18 optimal weight: 10.0000 chunk 27 optimal weight: 30.0000 chunk 129 optimal weight: 9.9990 overall best weight: 0.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.074574 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.067833 restraints weight = 16136.904| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.069208 restraints weight = 10171.812| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.070210 restraints weight = 6948.879| |-----------------------------------------------------------------------------| r_work (final): 0.3357 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7021 moved from start: 0.8302 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.028 15120 Z= 0.163 Angle : 0.795 12.751 20515 Z= 0.386 Chirality : 0.043 0.227 2275 Planarity : 0.005 0.040 2630 Dihedral : 5.487 30.842 2095 Min Nonbonded Distance : 2.050 Molprobity Statistics. All-atom Clashscore : 17.08 Ramachandran Plot: Outliers : 0.54 % Allowed : 11.53 % Favored : 87.94 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.97 (0.19), residues: 1865 helix: -0.77 (0.21), residues: 565 sheet: -0.10 (0.32), residues: 255 loop : -1.99 (0.18), residues: 1045 =============================================================================== Job complete usr+sys time: 1765.39 seconds wall clock time: 33 minutes 44.36 seconds (2024.36 seconds total)